From chemistry-request@server.ccl.net Thu Oct 11 04:31:16 2001 Received: from mbx.unige.ch ([129.194.8.72]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9B8VFB19721 for ; Thu, 11 Oct 2001 04:31:16 -0400 Received: from CONVERSION-DAEMON.mbx.unige.ch by mbx.unige.ch (PMDF V6.0-025 #38753) id <0GL100D01902M8@mbx.unige.ch> for CHEMISTRY@ccl.net; Thu, 11 Oct 2001 10:31:15 +0200 (MEST) Received: from pcpym ([129.194.52.174]) by mbx.unige.ch (PMDF V6.0-025 #38753) with SMTP id <0GL100BQP902LV@mbx.unige.ch> for CHEMISTRY@ccl.net; Thu, 11 Oct 2001 10:31:14 +0200 (MEST) Date: Thu, 11 Oct 2001 10:31:05 +0200 From: Pierre-Yves Morgantini Subject: G98 ReadVector option of the IRC Keyword To: CHEMISTRY@ccl.net Message-id: <007401c1522f$11c135e0$ae34c281@unige.ch> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-Mailer: Microsoft Outlook Express 5.50.4807.1700 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal X-Comment: This message was scanned against viruses by mbx.unige.ch. Dear CCLers, I need help from a Gaussian Guru... We are trying to locate a transition state but we always obtain 2 imaginary frequencies corresponding to highly coupled normal modes. To eliminate one imaginary frequency, I want to try to use the ReadVector option of the keyword IRC in the Gaussian 98 A.7 package. However, the description of this option is very short in the Gaussian manual (Read in the vector to follow. The format is Z=Matrix (FFF(I),I=1,NVAR), read as (8F10.6).) and I do not know how to obtain the vector to follow from a frequency calculation. Are there Gaussian users with some experience using this option ? Any help/advice will be welcome. Thank you in advance. P.-Y. Morgantini ______________________________________________________________________ Pierre-Yves Morgantini / Assistant Professor University of Geneva / Department of Physical Chemistry 30, quai Ernest Ansermet / 1211 GENEVA 4 (Switzerland) Phone (41-22) 702 65 24 (direct) / (41-22) 702 61 11 Mobile (41-79) 449 10 51 / Fax (41-22) 702 65 18 E-Mail Pierre-Yves.Morgantini@chiphy.unige.ch ______________________________________________________________________ From chemistry-request@server.ccl.net Thu Oct 11 07:33:51 2001 Received: from hotmail.com ([64.4.37.231]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9BBXpB23209; Thu, 11 Oct 2001 07:33:51 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 11 Oct 2001 04:33:46 -0700 Received: from 133.11.92.210 by pv2fd.pav2.hotmail.msn.com with HTTP; Thu, 11 Oct 2001 11:33:45 GMT X-Originating-IP: [133.11.92.210] From: "tianxiao young" To: chemistry-request@ccl.net Cc: chemistry@ccl.net Subject: LJ parameters of Cd+ and Cd(2+) ion Date: Thu, 11 Oct 2001 11:33:45 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 11 Oct 2001 11:33:46.0197 (UTC) FILETIME=[96AA9850:01C15248] Dear all, Would you be kind to tell me the van der waals parameters of Cd+ and Cd(2+) ion? I need the VDW radius and epsilon energy to carry out the MD calculation. Thank you very much for your kind help. Best wishes, young _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Wed Oct 10 13:18:50 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9AHIoB21016 for ; Wed, 10 Oct 2001 13:18:50 -0400 Received: from trentu.ca ([204.225.12.60]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K9C07EQFAG000L6J@trentu.ca> for chemistry@ccl.net; Wed, 10 Oct 2001 10:43:17 EDT Date: Wed, 10 Oct 2001 10:44:24 -0400 From: elewars Subject: charges on sphere, 3 more To: chemistry@ccl.net, koldham@trentu.ca, elewars@trentu.ca Message-id: <3BC45EC8.574F2E56@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2001 Oct 10 Hello, Here are three more responses to the charges on a sphere problem; they came in after I posted the Summary. Again, thanks to all who contributed. E. Lewars ====================== #1a Hi! I am out of this field for several years now, but this is my 2 cents worth of info... The problem you describe is a bit "classical". I remember a paper written within the last 20 years in either Science or Nature that addressed a similar problem. The issue then was at what "n" did you achieved a lower energy configuration by moving a point charge from the surface of a sphere to within the sphere. (Or something along this line of inquiry.) I tried looking for the paper in old boxes in the attic without success! Blah! Sorry! You may want to do a literature search on the topic of electrostatics and focus on Science and Nature. Good Luck! ===== -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Hillcrest Medical Center (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' Tulsa X-Ray Laboratory ((,.-' ((,/ 5840 South Memorial Suite 301 gamercier@yahoo.com Tulsa, OK 74145-9082 voice: 918-664-9892/fax: 918-664-6120 -------------- #2a I am only a chemist; but most of the answers do not convince me from a mathematical point of view: show the answer to math specialists before writting on the list! I am not convince when you (explicitly or implicitly) add the last charge to the n-1 previous ones, just because geometries can be very different in the n and n-1 cases. It is neither a simple mathematical problem to put small spheres on a big one. Pierre Vitorge CEA Saclay DEN/DPC/SCPA/LCRE Bat.450 pce 157D UMR 8587 (Universite d'Evry-CNRS-CEA) 91191 Gif sur Yvette cedex France pierre.vitorge@cea.fr phone +33 169-08-32-65, secretary: +33 169-08-32-50, fax: +33 169-08-32-42 http://perso.club-internet.fr/vitorgen/pierre/pierre.html pierre.vitorge@laposte.net ------------------------------------------- #3 Hi Errol, You may remember that we met when I visited Trent in February. With respect to the question you posted on CCL, I suggest you look at T.W. Melnyk, O. Knop and W.R. Smith, Can. J. Chem. 55, 1745 (1977). With best wishes, Russ Russell J. Boyd, Chair and Alexander McLeod Professor of Chemistry Department of Chemistry Dalhousie University Halifax, Nova Scotia Canada B3H 4J3 Tel: 902-494-3707 or 8883 Fax: 902-494-1310 ========================== ===================== From chemistry-request@server.ccl.net Wed Oct 10 15:24:06 2001 Received: from transmail12.infosources.fr ([212.232.33.78]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9AJO5B27616 for ; Wed, 10 Oct 2001 15:24:05 -0400 Received: from infonie.fr (mailbox.infonie.fr [195.242.64.77]) by transmail12.infosources.fr (8.11.6/8.11.6) with SMTP id f9AJO4920360 for ; Wed, 10 Oct 2001 21:24:04 +0200 (MEST) Received: from gros-bill.worldonline.fr ( Unverified [195.242.88.209] ) by infonie.fr with SMTP id 3195.7645936.232359; Wed, 10 Oct 2001 21:24:04 +0200 Message-Id: <5.1.0.14.0.20011012150831.00a126c0@pop.infonie.fr> X-Sender: twno3732@pop3.worldonline.fr (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 12 Oct 2001 15:21:54 +0200 To: chemistry@ccl.net From: Vanola Voravong Subject: Electrostatic interaction Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear all, Being new to the field of Intermolecular Forces, i am reading the great book of Stone ("The Theory of Intermolecular Forces"). I have questions about the optimum choice of origin when dealing with the electrostatic interaction between two molecules A and B. First, what is A (resp. B) ? Is it the centre of charges surrounding A (resp. B), its centre of symmetry, its centre of mass ? Second, where should we put the absolute origin ? On A or B ? On their centre of charges, symmetry, mass ? What are the best of these choices, for example, when A and B are two atomic ions (e.g He+ interacting with Li2+) ? Thanks for any help, Vanola From chemistry-request@server.ccl.net Wed Oct 10 17:26:41 2001 Received: from hotmail.com ([216.33.241.238]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9ALQeB01328 for ; Wed, 10 Oct 2001 17:26:40 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 10 Oct 2001 14:26:35 -0700 Received: from 134.129.118.146 by lw8fd.law8.hotmail.msn.com with HTTP; Wed, 10 Oct 2001 21:26:35 GMT X-Originating-IP: [134.129.118.146] From: "xin hu" To: chemistry@ccl.net Cc: xin.hu@ndsu.nodak.edu Subject: Why integral charges needed in AutoDock3.0 Date: Wed, 10 Oct 2001 21:26:35 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 10 Oct 2001 21:26:35.0321 (UTC) FILETIME=[3D1A7290:01C151D2] Hello, AutoDock user: I have a question about the charges of macromolecules used in AutoDock. Why it must be integral? I got the error warning with non-integral charges of protein (for some residues such as GLU the charge is -0.999 rather than -1.0), but I can still run the AutoDock and nothing different with the result. The same thing for the ion such as Mg. I assign an ab intio derived charge with +0.8e (for example) rather than +2.0, It is non-integral, but I found it is working well. Would someone please tell me why? Thanks for your help. Xin Hu Department of Pharmaceutical Sciences College of Pharmacy North Dakota State University Fargo, ND 58105 ---------------------------------------------------------- _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Wed Oct 10 18:36:55 2001 Received: from relay1.scripps.edu ([137.131.200.29]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9AMasB04314 for ; Wed, 10 Oct 2001 18:36:54 -0400 Received: from goliath.scripps.edu (goliath.scripps.edu [137.131.108.88]) by relay1.scripps.edu (8.11.6/TSRI-4.0.1r) with ESMTP id f9AMam528898; Wed, 10 Oct 2001 15:36:48 -0700 (PDT) Received: from goliath (goliath [137.131.108.88]) by goliath.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id PAA1606615; Wed, 10 Oct 2001 15:36:30 -0700 (PDT) Date: Wed, 10 Oct 2001 15:36:30 -0700 From: "Garrett M. Morris" To: "C. Michael McCallum" cc: ranjan@iitk.ac.in, CCL List Subject: Re: CCL:Running Autodock3 under linux2 In-Reply-To: <20011010094019.A11790@onsager.cop.uop.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There appears to be a great need for this nugget of information: to remove the limit on the stack size in Linux, type this simple command at your prompt: % limit stacksize unlimited Even better, add this line to your .login/.cshrc/.profile: limit stacksize unlimited This command will work on Linux, UNIX and Mac OS X (the "X" is pronounced "ten"). AutoDock will run on Mac OS X, by the way. This should permit your system to run AutoDock, assuming you have enough RAM. (You can check if an executable is too big by using the "size" command, e.g. "size autodock3". If you don't have enough RAM, recompile the AutoGrid and AutoDock programs after you have reduced MAX_GRID_PTS to 32 in "constants.h" - this will reduce the number of points you can use in your grid maps. It might be also be worth investing in more RAM.) Happy docking, :) Garrett On Wed, 10 Oct 2001, C. Michael McCallum wrote: > * ranjan@iitk.ac.in (ranjan@iitk.ac.in) [011009 10:56]: > > Hi David, > It seems to be a general problem for linux users. > > Actually the problem is with smaller stack size in linux.So set > > the stack size > > to a larger size. > > type in the shell: > > ulimit -s 66666 > > the value is essentially any thing you like ( i.e of the order of 60 MB here) > > Thr default for linux is 8MB. Keep increasing the stack size till it does not > > give core dump. > > It should help.. > > > > Chinmoy Ranjan, > > Chinmoy, this is a great general tip! But does anyone know how to set the > corresponding ulimit using csh or tcsh? The default for linux is indeed set > at 8M; How can a csh or tcsh user set it higher (or unlimited)? Is there a > system-wide setting for this? Anyone? > > Cheers, > > Mike McCallum > > -- > C. Michael McCallum | "That may be one tough nut to crack, > Associate Professor | but I am one determined > Chemistry, UOP | little squirrel" > mmccallum@uop.edu | (209) 946-2393 | fax (209) 946-2607 > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > Best wishes, Garrett ___ Dr Garrett M. Morris, MA, DPhil The Scripps Research Institute, tel: (858) 784-2292 Dept. Molecular Biology, MB-5, fax: (858) 784-2860 10550 North Torrey Pines Road, email: garrett@scripps.edu La Jolla, CA 92037-1000, USA. www.scripps.edu/pub/olson-web/gmm From chemistry-request@server.ccl.net Wed Oct 10 21:18:42 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9B1IgB10299 for ; Wed, 10 Oct 2001 21:18:42 -0400 Received: from trentu.ca ([204.225.12.60]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K9CMCF6UO4000MXG@trentu.ca> for chemistry@ccl.net; Wed, 10 Oct 2001 21:17:16 EDT Date: Wed, 10 Oct 2001 21:18:23 -0400 From: elewars Subject: Re: CCL:charges on sphere, summary To: Ivan Tubert , chemistry@ccl.net, koldham@trentu.ca Message-id: <3BC4F35E.2CB4DBB1@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: Hello, Thank you for your very interesting contribution to this discussion; and your idea of _simulating_ the situation is novel. I am passing on your response to the CCL net and to my colleague. E. Lewars ===== Ivan Tubert wrote: > Hi, > > I have a new response about the charge problem. > > Qualitatively, I think that they should all, or maybe all but one, be on > the surface. > > * We know that for small n, such as n=2, they are all on the surface. > > * In the limit n->infinity, if we assume that we have the charges on the > surface and add a new one, we have that the potential energy inside the > sphere is constant (it is the classical example of a charged sphere). > > * Therefore, when adding a new charge it would make no difference whether > we add it to the surface or inside the sphere. Let's assume we add it > to the center of the sphere, just for the sake of argument. However, we > cannot have two charges inside the sphere because they would repel each > other just as in the case n=2. > > So, for very large n, we would have n-1 charges on the surface, and one > "free" charge. > > This does not look like a formal proof, of course. So I decided to make an > "experiment" with a simple computer simulation. I wrote a program to > optimize the energy of the system by simulated annealing, and the results > up to n=100 always end up with all of the charges on the surface. However, > for large n, the last few charges (and especially the last one) take a > while to migrate to the surface, seemingly in agreement with the concept > of "one free charge". > > The program is written in C, is not user-friendly, and surely it is very > inefficient (I would not recommend trying to optimize n > 100). You > have to edit the source and compile it to change the parameters, but I > include the source as an attachment in case you are interested. > > Regards, > Ivan Tubert > > ------------------------------------------------------------------------ > > #include > > #include > > #include > > #include > > #include > > #include > > typedef struct { > > double x, y, z; > > double q; > > } PARTICLE; > > typedef struct { > > double r, theta, phi; > > } POLAR; > > #define PI 3.1415926535 > > /************* PARAMETERS ***********/ > > double r = 1.0; // radius of the sphere > > double k = 1.0e-4; // "Boltzmann constant" > > double stepsize = 0.005; // size of random move > > double T0 = 1000.0; // initial temperature > > double DT = 50.0; // temperature step > > int NSTEPS = 5000; // number of moves for each temperature > > int NPART = 48; // Number of particles > > /************************************/ > > double get_r(PARTICLE p) > > { > > return(sqrt(p.x*p.x+p.y*p.y+p.z*p.z)); > > } > > PARTICLE *init(int n, double q) > > { > > int i; > > PARTICLE *p; > > p = malloc(sizeof(PARTICLE)*n); > > assert (p); > > for(i = 0; i < n; ++i){ > > p[i].q = q; > > do { > > p[i].x = (1.0*rand()/RAND_MAX - 0.5) * 2 * r; > > p[i].y = (1.0*rand()/RAND_MAX - 0.5) * 2 * r; > > p[i].z = (1.0*rand()/RAND_MAX - 0.5) * 2 * r; > > } while (get_r(p[i])>r); > > } > > > > return p; > > } > > double get_dist(PARTICLE p1,PARTICLE p2) > > { > > return( sqrt((p1.x-p2.x)*(p1.x-p2.x)+(p1.y-p2.y)*(p1.y-p2.y)+(p1.z-p2.z)*(p1.z-p2.z)) ); > > } > > double get_E(PARTICLE *p) > > { > > int i,j; > > double E = 0.0; > > for(i = 0; i < NPART-1; ++i){ > > for(j = i+1; j < NPART; ++j){ > > E += p[i].q*p[j].q/get_dist(p[i], p[j]); > > } > > } > > return E; > > } > > POLAR get_polar(PARTICLE p) > > { > > POLAR pol; > > pol.r = get_r(p); > > pol.theta = acos(p.z/pol.r); > > pol.phi = atan(p.y/p.x); > > if(p.y < 0) > > pol.phi += PI/2; > > return pol; > > } > > void get_stat_r(PARTICLE *p, double *mean, double *sd) > > { > > int i,j; > > double r = 0.0, r2 = 0.0, d; > > > > for(i = 0; i < NPART-1; ++i){ > > for(j = i+1; j < NPART; ++j){ > > d = get_dist(p[i], p[j]); > > r += d; > > r2 += d*d; > > } > > } > > *mean = 2*r/NPART/(NPART-1); > > *sd = sqrt(2*r2/NPART/(NPART-1) - *mean * *mean); > > } > > void print(PARTICLE *p) > > { > > int i; > > POLAR pol; > > double mean, sd; > > printf(" x y z -> r theta phi\n"); > > for(i = 0; i < NPART; ++i){ > > pol = get_polar(p[i]); > > printf("%8.2f%8.2f%8.2f -> %8.2f%8.2f%8.2f\n", p[i].x, p[i].y, p[i].z, pol.r, pol.theta, pol.phi); > > } > > > > get_stat_r(p, &mean, &sd); > > printf(" mean radius r(ij) = %5.2f +/- %5.2f\n", mean, sd); > > } > > int main() > > { > > double T; > > int i; > > PARTICLE *p, newp, oldp; > > double oldE, newE; > > int ip; > > double bz,rn; > > int reject; > > > > srand( (unsigned int)time( NULL ) ); > > T = T0; > > p = init(NPART, 1.0); > > newp.q = 1.0; > > print(p); > > oldE = get_E(p); > > while(T >= 0.0) { > > reject = 0; > > printf("T = %5.f ... ", T); > > for(i = 0; i < NSTEPS; ++i){ > > ip = rand()%NPART; > > do { // move > > newp.x = p[ip].x + (1.0*rand()/RAND_MAX - 0.5) * 2 * stepsize; > > newp.y = p[ip].y + (1.0*rand()/RAND_MAX - 0.5) * 2 * stepsize; > > newp.z = p[ip].z + (1.0*rand()/RAND_MAX - 0.5) * 2 * stepsize; > > } while (get_r(newp)>r); > > oldp = p[ip]; > > p[ip] = newp; > > newE = get_E(p); > > if(newE > oldE){ > > bz = exp((oldE-newE)/k/T); > > rn = 1.0*rand()/RAND_MAX; > > if (rn > bz) { // reject > > p[ip] = oldp; > > newE = oldE; > > ++reject; > > } > > } > > > > oldE = newE; > > } > > T -= DT; > > printf("Rejected %i moves out of %i\n", reject, NSTEPS); > > print(p); > > } > > > > return(0); > > } From chemistry-request@server.ccl.net Thu Oct 11 09:53:04 2001 Received: from darwin-hme0.sepracor.com ([65.195.118.2]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9BDr3B27058 for ; Thu, 11 Oct 2001 09:53:03 -0400 Received: from mailhost.sepracor.com by darwin-hme0.sepracor.com via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 11 Oct 2001 14:49:16 UT Received: from newton.sepracor.com by lovelace-qfe0 via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 11 Oct 2001 13:53:04 UT Received: by newton.sepracor.com with Internet Mail Service (5.5.2653.19) id ; Thu, 11 Oct 2001 09:51:33 -0400 Message-ID: <112AF07B6833D511B45300104BC6AD5102FEE9@newton.sepracor.com> From: Gerry Tanoury To: "'chemistry@ccl.net'" Subject: Molecular radius for organic solvents Date: Thu, 11 Oct 2001 09:51:30 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, I am performing some calculations using the COSMO solvation model. One of the parameters defines the solvent's molecular radius. Is there a place where I can find the molecular radii of common organic solvents? I am especially interested in toluene. Kind regards, Gerald J. Tanoury, Ph.D. Principal Research Chemist Sepracor Inc. 111 Locke Dr. Marlborough, MA 01752 Ph: (508) 357-7442 Fax: (508) 357-7808 E-mail: gtanoury@sepracor.com From chemistry-request@server.ccl.net Thu Oct 11 10:03:27 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9BE3RB27392 for ; Thu, 11 Oct 2001 10:03:27 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id KAA23269; Thu, 11 Oct 2001 10:03:27 -0400 (EDT) Date: Thu, 11 Oct 2001 10:03:27 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: jonathan.hirst@nottingham.ac.uk Subject: 02.07.31 Exploring Modern Computational Chemistry, U Nottingham Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Thu, 11 Oct 2001 14:52:44 +0100 From: Jonathan Hirst To: jkl@ccl.net Subject: conference announcement Conference announcement Exploring Modern Computational Chemistry 31st July - 2nd August, 2002 University of Nottingham, UK. For more details and pre-registration please visit: www.nottingham.ac.uk/chemistry/emc2 Organised in association with the Royal Society of Chemistry Theoretical Chemistry Group. Sponsored by Q-Chem Inc., Collaborative Computational Projects CCP5 and CCP6. Official satellite meeting of WATOC'02 This international conference will bring together researchers in all aspects of modern computational chemistry. The programme will consist of invited lectures and a Poster session, which will be an integral part of the programme. Scientific Topics will include: Quantum Chemistry, Density Functional Theory, Structure and Spectroscopy, Intermolecular Potentials, Statistical Thermodynamics, Biological Applications. Speakers who have accepted invitations include: A. Alavi (Cambridge), A. D. Becke (Queens', Ontario), C. R. A. Catlow (Royal Institution of Great Britain), D. C. Clary (University College London), J. N. L. Connor (Manchester), H. H. Fielding (King's College London), G. Frenking (Marburg), J. Gauss (Mainz), N. C. Handy (Cambridge), M. Head-Gordon (Berkeley), T. U. Helgaker (Oslo), I. H. Hillier (Manchester), K. N. Houk (UCLA) , W. M. Klopper (Utrecht), D. E. Logan (Oxford), R. M. Lynden-Bell (Queen's University Belfast), F. Manby (Bristol), A. B. McCoy (Ohio State), J. N. Murrell (Sussex), M. Orozco (Barcelona), J. A. Pople (Northwestern), S. L. Price (University College London), L. Radom (Australian National University), H. F. Schaefer III (Georgia), K. Szalewicz (Delaware), I. H. Williams (Bath), W. F. van Gunsteren (ETH). Nottingham is at the centre of the United Kingdom and is well linked by air, road and rail to major UK and European cities. The East Midlands International Airport is just 20 minutes drive away. The area offers many tourist attractions and is well known throughout the world through the legend of Robin Hood. Nottingham offers a large and diverse range of shopping facilities plus a lively nightlife and wide variety of restaurants. The University campus is situated three miles from Nottingham city centre and is set in a belt of woodland, parks and playing fields covering 330 acres. -- Conference: Exploring Modern Computational Chemistry, Nottingham 2002 http://www.nottingham.ac.uk/chemistry/emc2 Dr Jonathan Hirst School of Chemistry, University of Nottingham University Park, Nottingham NG7 2RD Tel: +44 115 951 3478; FAX: +44 115 951 3562 Email: jonathan.hirst@nottingham.ac.uk URL: www.nottingham.ac.uk/chemistry/staff/hirst/hirst.html From chemistry-request@server.ccl.net Thu Oct 11 11:52:32 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9BFqVB30241 for ; Thu, 11 Oct 2001 11:52:31 -0400 Received: from sun4.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Thu, 11 Oct 2001 17:52:31 +0200 Received: from localhost (ui22204@localhost) by sun4.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id RAA06715 for ; Thu, 11 Oct 2001 17:52:29 +0200 (MET DST) X-Authentication-Warning: sun4.lrz-muenchen.de: ui22204 owned process doing -bs Date: Thu, 11 Oct 2001 17:52:29 +0200 (MET DST) From: Eugene Leitl X-X-Sender: To: Subject: FYI:[Open-Bioinformatics-Foundation] All Project Open-Bio Newsletter(long) (fwd) Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Wed, 10 Oct 2001 15:20:16 -0400 (EDT) From: Chris Dagdigian To: open-bioinformatics-foundation@open-bio.org Subject: [Open-Bioinformatics-Foundation] All Project Open-Bio Newsletter (long) This email is being sent to every person who is subscribed to one of the discussion or announce lists that we host. Rather than cross post to 31 individual mailing lists we merged all the subscribers into a unique list. This helps to keep our active volunteers from getting many copies of the same message. =========================================================================== (O|B|F) Open Bioinformatics Foundation N E W S L E T T E R October 2001 http://open-bio.org biopython.org, biojava.org, bioperl.org bioXML.org, bioCORBA.org, bioDAS.org, biomoby.org, etc. =========================================================================== Introduction There has been very significant progress and change within our project(s) and organizational ranks lately; most of these changes not been immediately obvious or visible on our web sites or mailing lists. This email message is our first attempt at what will hopefully become a regular update on the 'big picture' status of our projects and efforts. If you have comments, questions or concerns about anything in this newsletter you can email the Open-Bio board directly at Summary of topics in today's message: o Organizational Status - Our cross-project name is now the "Open Bioinformatics Foundation" - O|B|F is now a non-profit corporation - 2001/2002 Board of Directors announced - Legal services provided pro bono by HellerEhrman o Organizational Financial Summary - Current funds - BOSC'2001 profit o Server and Connectivity Update o Current & New project briefs - New efforts: bioMOBY & bioSOAP o Upcoming Events - ORA Bioinformatics Technology Conference + BOF leaders needed ASAP - Open-Bio Hackathon(s) + Phoenix, Arizona + Cape Town, South Africa o Call for Volunteers ------------------------------------------------------------------------- ORGANIZATIONAL STATUS & NEW LEGAL REPRESENTATION ------------------------------------------------------------------------- Over the past few years an informal group of volunteers and open-bio project leaders has self-formed to handle issue that span all of our current projects. Many of these new needs came about as we began to 'own' assets such as servers and domain names and others happened once we began organizing bootcamps and conferences and found ourselves having to sign binding legal and financial agreements. This group has also handled all the behind the scenes work necessary to keep our servers and Internet connectivity running smoothly. It has become obvious over the past year that this "umbrella" group while functional could benefit greatly from a more formal organizational structure. Long talked about it was finally decided at BOSC'2001 in Copenhagen that we should take the plunge and incorporate the group as a formal not-for-profit entity. The goals of the new organization are the same as before: providing administrative, financial and technical support to our ongoing and future projects. The new entity will be called the "Open Bioinformatics Foundation" The current Directors for 2001/2002 are as follows: - Ewan Birney (European Bioinformatics Institute) - Steven E. Brenner (University of California, Berkeley) - Andrew Dalke (Dalke Scientific Software, LLC ) - Chris Dagdigian (Blackstone Computing Inc.) - Hilmar Lapp (Novartis Research Foundation) The Directors have chosen corporate Officers for the following positions: - Ewan Birney, President & Chief Executive Officer - Chris Dagdigian, Treasurer & Chief Financial Officer - Andrew Dalke, Secretary A rented mailbox serves as our official corporate address: Open Bioinformatics Foundation 411A Highland Avenue #318 Davis Square Somerville, MA 02144 Phone/Fax 617-250-0000 x4327 As of October 4th 2001 the Open Bioinformatics is a not-for-profit company incorporated in the state of Delaware. More info and links to our meeting minutes and organizational bylaws will be forthcoming. New Legal Representation for the organization As part of the ongoing attempts to get ourselves organized we are very pleased to announce that we now have top-notch legal assistance being provided pro-bono by the law firm HellerEhrman (http://www.hewm.com) In particular we'd like to acknowledge the assistance and guidance of Dan Appelman who co-chairs the IT National Practice Group at HellerEhrman. His attorney bio can be read online at http://www.hewm.com/attorneys/attorneyBio.asp?attorneyID=341 ------------------------------------------------------------------------- FINANCES ------------------------------------------------------------------------- Our current bank account is the same one we have been using for several years-- a "Small Business" account registered to "The BioPerl Project" held at a bank in Massachusetts, USA. After the corporation is fully formed it is likely that will close this account and open a new "Open Bioinformatics Foundation" account. Our current bank balance is approximately $7000 USD of which most is earmarked to pay for BOSC'2000 facility expenses that UCSD is very late in billing us for. This means that practically speaking we have less than $1000 USD free cash at the moment. Most if not all of that remaining money will be used to pay filing fees and expenses associated with incorporating the non-profit company. Sun Microsystems had provided significant financial support to offset BOSC'2001 expenses. We have invoiced them for the full amount but won't consider it 'real money' until we receive the funds. Future expenses that we foresee: o Misc. hardware & gear needed for racking our new server systems o Getting a Sun hardware support contract for the donated systems o Purchase/renewal of domain names o Supporting hackfests & misc. activities Needless to say cash or hardware donations are welcome. BOSC'2001 (Copenhagen) Financial Summary Despite a very successful conference in Copenhagen we had some significant expenses caused mainly by the requirement that we use the designated ISMB conference company to handle registration and AV rental support. Our goal in general with BOSC meetings is to make the registration fee as low as possible while trying to ensure that we don't actually lose any money. We have made a small profit at each of the last 2 conferences. BOSC'2001 (Denmark) Conference financial breakdown: Total number of attendees: 163 Our fixed costs per attendee were 880 DKK per person Income received: Academic: 57 @ 1100 DKK = 62700.00 DKK Corporate: 68 @ 1400 DKK = 95200.00 DKK Student: 38 @ 880 DKK = 33440.00 DKK Total income: 191340.00 DKK Expenses: Meeting expenses (fixed) 158933.00 DKK Extra AV costs 19582.00 DKK Poster stands 2640.00 DKK Extra flipcharts 594.00 DKK Total expenses: 181749.00 DKK BOSC'2001 PROFIT: 9591.00 DKK ($1,177.00 US Dollars) BOSC Pictures available at http://open-bio.org/bosc2001/bosc2001_pics/ ------------------------------------------------------------------------- SERVER & CONNECTIVITY UPDATE ------------------------------------------------------------------------- Our upstream provider of donated internet bandwidth is upgrading its internet connection through October and November. There may be downtime or sporadic connectivity outages as this effort progresses. If we need to change the IP addresses of our servers the downtime may last 8-24 hours as the new domain info propagates outward. Thanks again to Genetics Institute / Wyeth Ayerst Research we now have secure space in which to begin unpacking and building our new server hardware. A short list of the hardware we have available is as follows: o 3 Sun Netra T1000 high density rackmount servers o 1 Sun Netra A1000 UltraSCSI RAID array o 1 Cobalt Raq 4 rackmount server appliance o 1 VALinux 1220 high density PentiumIII rackmount server Our current plans are to split the multiple servers out according to task: 1) Web, email listserv, DNS & FTP services 2) Core project(s) server with RAID for our source code and developers 3) anonymous CVS front-end and nightly build system A firewall/IDS system is being worked on as a separate project. We will be building, integrating and rolling out these systems in stages over the next several months. Expect to see a few more announcements and solicitations for volunteer assistance as things get under way. We need people with Solaris Admin skills to help us build, tune and secure the Netra servers. See the section below on "Volunteers" for more information or contact Chris Dagdigian directly at dag@sonsorol.org. New hardware pictures are online. We will be updating this URL as the build out of our new server systems continues: ** http://open-bio.org/Hardware-pics/ ** Some website statistics: Apache Server Statistics as of 2 October 2001 Server uptime: 16 days 15 hours 11 minutes 9 seconds Total accesses: 146,749 - Total Traffic: 2.4 GB Bioperl.org Website stats 1 Year Average: 98,172 hits/month 59,925 pageviews/month Sep 2001 : 62,125 hits, 874,361 KB transferred, 86 hits/hour avg Biojava.org Website stats 1 Year Average: 57,475 hits/month 34,389 pageviews/month Sep 2001 : 66,418 hits, 2,291,842 KB transferred, 92 hits/hour avg ------------------------------------------------------------------------- INCOMPLETE PROJECT BRIEFS & ANNOUNCEMENT OF NEW PROJECTS ------------------------------------------------------------------------- o Biopython Biopython is rapidly approaching a 1.0 release with a maturing sequence model, support for pathways, a new parsing framework (Martel), and algorithms for sequence computation and alignment. Currently, we are adding support for more file formats and implementing more algorithms. As always, volunteers are welcome. In addition to coders, we also need people to work on testing, documentation, and web development. o Biojava Since the 1.1 release earlier this year, the emphasis of BioJava development has been on improved connectivity (DAS, Ensembl), and better flatfile parsers (EMBL, Genbank, Blast). In the future we hope to see more support for ontologies, and a more general query mechanism. There is also a group interested in developing an object model for expression data. All contributions are welcome, whether documentation, code, or suggestions. Additional tutorials are always extremely welcome! o Biocorba The BioCORBA project has seen increased activity after building numerous prototype and production servers. Previously, two standards for biological objects in CORBA existed from the BioCORBA project and the BSA and BSANE proposals from the LSR group of the OMG (http://lsr.omg.org). After the meetings held at ISMB 2001 in Copenhagen, Denmark (dubbed the "Tivoli Meetings") a compatible proposal was agreed upon which combined these two standards. Work is under way in the Perl and Python camps to implement these standards. There is a need for Java volunteers to implement a BioJava <-> BioCorba bridge in the months to come. The end result of these standards will allow seamless launching of analysis applications in perl,python,and java (even C if someone wants to implement the client side). Connections to sequence (EMBL, NCBI) and annotation sources (Ensembl, Flybase, WormBase) will allow developers to integrate data sources with analysis systems. This will further simplify the establishment of pipelines for both small laboratories and large institutions which wish to rely on open-bio toolkits for their informatics needs. Tutorials and Full documentation are being generated as well as skeleton programs to serve as examples. Opportunities for volunteers exists in every aspect of the project and from evaluating the BioCORBA/BSANE standard to writing client/server software to helping produce documentation and testing applications for portability and ease of use. o Bioperl The Bioperl project continues to expand and address more needs of biological researchers. New developers and contributors to the mailing lists have furthered the scope of the project and seek to address new areas of data from microarray, phylogenetics, bibliographic, and annotation sources as well as integrate with more external applications. Recent work has produced modules suitable for retrieving sequences from online sources such as swissprot and EMBL. One can also submit analysis jobs to online analysis queues such as NCBI's blast queue and soon we will have build access to EBI applab analysis through the NOVELLA CORBA interfaces. New work is focusing on standardizing input and output methods to these application servers. Additional resources for local DAS servers in bioperl have been submitted and will be part of the next major release of bioperl. We expect the 1.0 release to be completed by the end of 2001 and will continue to be a stable platform for bioinformatics software development in perl. The 0.7.2 stable release is expected to be released in mid November and will correct a number of small bugs in the 0.7.1 release. Developer releases (0.9.x unstable series) will continue to be released until the 1.0 release and serve as snapshops of working code in the release that passes all bioperl tests. o BioXML o BioDAS Two new efforts have been initiated recently o BioMOBY (http://biomoby.org) ** site online ** BioMOBY is an international group of biological data hosts, biological data service providers, and coders whose aim is to achieve a maximum amount of data interoperability between host institutions. The website provides an online resource for modules, scripts, and schema for developers of MOBY-related software. CVS access will be available shortly. BioMOBY project admin: Mark Wilkinson o BioSOAP (http://biosoap.org) ** future site ** biosoap.org will aim to develop a bridge system between the core objects of bioperl and biojava as well as between the current perl-based Ensembl and the upcoming java port of it. It will hopefully allow such things as perl scripts running with java objects, as well as over-the-net object oriented programming. It is in its infancy, so any support, advice and suggestions will be most appreciated. BioSOAP project admin: Elia Stupka o biostandards.org We've had this domain name for a while and have done nothing with it. Suggestions welcome. ------------------------------------------------------------------------- UPCOMING EVENTS ------------------------------------------------------------------------- 2-Part Open Bioinformatics Hackathon in USA and South Africa ! This is an early sneak-peek announcement. Details will follow from the actual organizers. O'Reilly & Associates (http://www.ora.com) and Electric Genetics (http://www.egenetics.com) are going to jointly hold two open-bio hackathons. The hackfest will start with a three-day event as part of the O'Reilly Bioinformatics Technology Conference in Arizona in late January and continue with a seven-day session in Cape Town, South Africa scheduled for late February. The event is invitation only and attendees will have all travel and accomodation expenses paid. This is very exiting news, more details will be announced. Open-Bio at the O'Reilly Bioinformatics Technology Conference, Jan 2002 Conference site: http://conferences.oreilly.com/biocon/ It appears that many of our project admins and developers are going to be attending the ORA conference in January. Ewan Birney is giving a keynote address and several Open Bio people are giving talks and/or tutorials at the conference. In addition to the tutorial sessions, the OBF will also have a conference booth in the exhibit hall and we have been invited by the conference staff to organize and host informal Bird Of a Feather ("BOF") sessions as necessary. We have already committed to hosting the following BOF sessions at the conference: o Bioperl developers o new Bioperl users o Biopython users & developers HOST YOUR OWN BOF! If you are interested in hosting/moderating a gathering of like-minded individuals at the conference please respond to Andrew Dalke . We need to know (a) who you are and (b) what BOF topic you propose to host. ------------------------------------------------------------------------- CALL FOR VOLUNTEERS ------------------------------------------------------------------------- We always welcome volunteers and are soliciting people right now for the following roles and projects: * Volunteer Coordinator This person or group would be responsible for monitoring a new email address we are going to set up called "volunteer@open-bio.org". The coordinators will screen & manage volunteer offers, match them to current projects/needs and otherwise help with orientation and introductions. Time commitment: Minimal How to sign up : email board@open-bio.org * Webteam (architect & deploy a new website for us) The problem is simple. Our web presence sucks. We need something better. The task of the webteam is to come up with a plan and follow it through. Time commitment: depends; may be significant in the early stages How to sign up: email volunteer@open-bio.org * Mailteam We use the GNU Mailman system for our mailing lists. It is a nice piece of software that can be almost entirely administrated via a web interface. Once the lists are created they are largely self-operating. We occasionally need an administrator to respond to user question, manually unsubscribe the clueless and act as moderators when our spam mail filters quarantine suspect messages. We are looking to set up a small group of people who monitor and moderate the dozens of mailing lists we have currently running. Time commitment: minimal How to sign up: email volunteer@open-bio.org * SolarisGurus A significant amount of our new server hardware will run Solaris. We need people who are available to answer configuration questions, idiot check changes and help with securing each box. Time commitment: depends; may be significant in the early stages How to sign up: email volunteer@open-bio.org * CambridgeTeam All of our existing and future server hardware is located in Cambridge, Massachusetts (subway accessible via the Red Line!). There may come a time where we need physical bodies to help rack servers or possibly transport the systems to new hosting facilities. We are attempting to get a sense of how many people we have local to the area that may be available if needed. Time commitment: probably zero How to sign up: email Chris Dagdigian _______________________________________________ Open-Bioinformatics-Foundation mailing list Open-Bioinformatics-Foundation@open-bio.org http://open-bio.org/mailman/listinfo/open-bioinformatics-foundation From chemistry-request@server.ccl.net Thu Oct 11 11:48:18 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9BFmHB30104 for ; Thu, 11 Oct 2001 11:48:18 -0400 Received: from sun4.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Thu, 11 Oct 2001 17:48:16 +0200 Received: from localhost (ui22204@localhost) by sun4.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id RAA06703 for ; Thu, 11 Oct 2001 17:48:15 +0200 (MET DST) X-Authentication-Warning: sun4.lrz-muenchen.de: ui22204 owned process doing -bs Date: Thu, 11 Oct 2001 17:48:15 +0200 (MET DST) From: Eugene Leitl X-X-Sender: To: Subject: FYI:Call-For-Participation: 2nd Workshop on Linux Cluster for SuperComputing (fwd) Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id f9BFmIB30105 -- Eugen* Leitl leitl ______________________________________________________________ ICBMTO: N48 04'14.8'' E11 36'41.2'' http://www.lrz.de/~ui22204 57F9CFD3: ED90 0433 EB74 E4A9 537F CFF5 86E7 629B 57F9 CFD3 ---------- Forwarded message ---------- Date: Wed, 10 Oct 2001 21:28:07 +0200 From: Niclas Andersson To: beowulf@beowulf.org Subject: Call-For-Participation: 2nd Workshop on Linux Cluster for Super Computing Call for Participation 2nd WORKSHOP ON LINUX CLUSTERS FOR SUPER COMPUTING Last date for registration: 15 october! ============================================================ -- 2nd WORKSHOP ON LINUX CLUSTERS FOR SUPER COMPUTING -- Clusters for applications and GRID solutions. 25-26 October 2001 Hosted by National Supercomputer Centre (NSC) Linköping University Sweden ============================================================ The fast development of the processing power of high-end PCs and workstations together with the availability of open source operative systems such as Linux have made it possible to build very cost effective parallel computers. With the addition of high band width networks with low latency PC-clusters are challenging conventional commercially available parallel computers. PC-clusters can in many cases yield orders of magnitude in prize performance. Assembling a PC-cluster is, however, a non-trivial task due to the fast moving PC and workstation market as well as the rapid development of Linux and available tools for clustered computing. The aim of the workshop is to gather together people with experience of clusters and provide participants with an overview of state of the art PC-clusters. The workshop will address the hardware and software issues encountered during design as well as some of the emerging application areas in which PC-cluster have been deployed. We intend to cover the following topics: o Distributed computing and GRID technologies o Update on the latest hardware developments o Tools for managing and using clusters o Scalability issues, benchmarking and tuning o Batch systems and job scheduling strategies o Key application areas We are very pleased to announce that Dr. MARK BAKER, University of Portsmouth, will give the workshop keynote address. Mark's current research is focused on the development of tools and services for PC-based distributed systems. Mark has written a number of articles and papers on Cluster and Grid Computing and is co-chair of the conference IEEE Cluster 2001. Furthermore, BEN SEGAL, CERN Information Technology Division, will give a talk on GRID technologies. Ben has been responsible for the buildup of many high speed networks at CERN. Until recently Ben managed the section Technologies for Experiments. Ben is now concentrating on managing the Data Management work package in the European DataGrid project. The complete list of speakers and programme will be available at http://www.nsc.liu.se/lcsc/. If you wish to present your own PC-cluster project or give a talk on a topic related to clustered computing please contact Niclas Andersson . CONFERENCE DETAILS Location The conference will take place at Collegium, Mjärdevi Science Park close to Linköping University. Registration The conference fee is SEK 1000 (+25% VAT) for industry, SEK 700 for academics, and SEK 300 for students. The fee covers conference administration, coffee and lunch on both days and dinner on Thursday evening. There is no fee for students who choose to attend the workshop but do not have lunch or dinner. Please register by Wednesday 10 October by supplying the following information either: - on line or - e-mail to or - mail to Nationellt Superdatorcentrum Attn: Anki Rune Linköpings Universitet 581 83 LINKÖPING *Name *Company *Address *Telephone *Fax *E-mail *Special dietary requirements, ie, vegetarian. *If you intend to have lunch on both days and dinner on the 25th. Further Information For more information, including hotel information please see http://www.nsc.liu.se/lcsc ---------------------------------------- Workshop on Linux Clusters for Super Computing 25-26 October 2001 National Supercomputer Centre (NSC), Linköpings University REGISTRATION FORM Name: Company: Student...........YES......NO Address: E-mail: Telephone: Fax: I will have lunch on 25 October.........YES....NO I will have dinner on 25 October........YES....NO I will have lunch on 26 October.........YES....NO Special dietary requirements, ie vegetarian................... ---------------------------- _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf From chemistry-request@server.ccl.net Thu Oct 11 12:29:14 2001 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9BGTEB31543 for ; Thu, 11 Oct 2001 12:29:14 -0400 Received: from I.T.S.ME ([129.43.27.170]) by kafka.net.nih.gov (8.11.3/8.10.1) with ESMTP id f9BGTDK08683; Thu, 11 Oct 2001 12:29:13 -0400 (EDT) Date: Thu, 11 Oct 2001 12:25:58 -0400 (Eastern Daylight Time) From: "M. Nicklaus" To: CHEMISTRY@ccl.net cc: mn1@helix.nih.gov Subject: SUMMARY: Chemistry Databases/Services (Small Molecule) on the Web Message-ID: X-X-Sender: mn1@helix.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A while ago, I posted the following question: ========================== QUESTION =========================== I'm trying to compile a list of all the Web sites offering chemical structural databases (small molecule) that have at least one of the following capabilities: - Search by (sub-) structure - Display of the structure, at least in 2D (not just a name) - Download/save a structure in a computer-readable format (SD, PDB...) - Retrieve/dump large parts of the database (or even the entire DB) in bulk form, again in a computer-readable format - Perform some kind of calculation on the structure (e.g. physicochemical properties etc.) - At least 100 molecules available - Accessible with just a Web browser, possibly with some easily obtainable plugin (this excludes services that require a special application, such as SciFinder) These sites may be academic, commercial, government, non-profit. Required fees or subscription is not a disqualifier, but should be noted. I already have a certain number of such URLs; but I want to make sure that I don't overlook anything. I'll post a summary of course. ========================== ANSWERS ============================ I got a few replies. Thanks to all who responded. S Bear pointed out his own list, which proved to be very useful for the compilation of our table. The three lists of links I found most useful in this context are: http://geocities.com/soaringbear/biomed/chem.html http://www.liv.ac.uk/Chemistry/Links/refdatabases.html http://chemfinder.cambridgesoft.com/siteslist.asp After quite a bit of additional hunting of my own, and trying to compare features to some extent, I've decided not to post an unwieldy table on the list. Instead, I have put up this table on our server, under: http://cactus.nci.nih.gov/ncidb2/chem_www.html. A note aside: Be forewarned - while testing all these sites, I experienced numerous plugin incompatibilities, web browser (if not OS) crashes, plugins "grabbing" files types/associations from each other etc. Now, with all the very latest plugin versions installed, things seem to be a bit more stable -- but this was not a wholly satisfactory experience... Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design MiniCore Facility Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Oct 11 15:18:06 2001 Received: from goodyear.goodyear.com ([209.57.161.2]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9BJI6B02974 for ; Thu, 11 Oct 2001 15:18:06 -0400 Received: from rdsrv7.goodyear.com by goodyear.goodyear.com via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 11 Oct 2001 19:18:07 UT Received: from [163.243.4.69] (rds325.goodyear.com [163.243.4.69]) by goodyear.com (8.9.1b+Sun/8.8.8) with ESMTP id PAA22876 for ; Thu, 11 Oct 2001 15:18:05 -0400 (EDT) User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Thu, 11 Oct 2001 15:18:05 -0400 Subject: Re: CCL:Molecular radius for organic solvents From: Craig Burkhart To: Message-ID: In-Reply-To: <112AF07B6833D511B45300104BC6AD5102FEE9@newton.sepracor.com> Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Gerry: A common method of computing the effective radius of a solvent (also works for solids, by the way) is by computing the effective volume of the solvent sphere: 4 Pi r_eff^3 = cnv 3 amu occ / rho, > from which it follows that r_eff = (r_eff^3 / (4 Pi))^(1/3), where r is the effective radius of the molecule in Angstroms, cnv is the conversion from cm^3 to Angstroms^3 (= 10^24 Ang^3/cm^3), amu is the atomic mass of the molecule (it's molar mass divided by Avagadro's number), occ is the packing density (assuming random close packing of spheres, this would be ~0.58; for a crystalline material this you might want to use the bcc occupancy, 0.680), and rho is the molecular density in gm/cc. If you use the above formula for water, you will note that it does not correspond (1.60 A for occ = 0.58; 1.53 for occ = 0.50) to the "reported" radius of 1.40 Angstroms. The reason why there is a discrepancy, to the best of my knowledge, is that the 1.40 A value is a "best fit" from water solvation simulations. In the absence of a "best fit" situation, I would suggest that you follow the above formula. For typical organic liquids, I use 0.58 as the occupation factor. Hope this helps. Craig Burkhart Goodyear Chemical R&D From chemistry-request@server.ccl.net Thu Oct 11 14:49:02 2001 Received: from ex1.ncsa.uiuc.edu ([141.142.2.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9BIn1B02333 for ; Thu, 11 Oct 2001 14:49:02 -0400 Received: from mx1.ncsa.uiuc.edu (mx1.ncsa.uiuc.edu [141.142.2.8]) by ex1.ncsa.uiuc.edu (8.11.6/8.11.0) with ESMTP id f9BIn1H17925; Thu, 11 Oct 2001 13:49:01 -0500 (CDT) X-Envelope-From: spamidig@ncsa.uiuc.edu Received: from sudhakardell.ncsa.uiuc.edu (sudhakardell.ncsa.uiuc.edu [141.142.65.106]) by mx1.ncsa.uiuc.edu (8.11.6/8.11.0) with ESMTP id f9BIn0311840; Thu, 11 Oct 2001 13:49:00 -0500 (CDT) Message-Id: <5.1.0.14.2.20011011134915.01d79fc0@pop.ncsa.uiuc.edu> X-Sender: spamidig@pop.ncsa.uiuc.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 11 Oct 2001 13:50:45 -0500 To: "M. Nicklaus" , CHEMISTRY@ccl.net From: Sudhakar Pamidighantam Subject: Re: CCL:SUMMARY: Chemistry Databases/Services (Small Molecule) on the Web Cc: mn1@helix.nih.gov In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed http://chemviz.ncsa.uiuc.edu is mainly intended for education, which can be/will be easily enhanced for research. Sudhakar. At 12:25 PM 10/11/2001 -0400, M. Nicklaus wrote: >A while ago, I posted the following question: > >========================== QUESTION =========================== >I'm trying to compile a list of all the Web sites offering chemical >structural databases (small molecule) that have at least one of the >following capabilities: > >- Search by (sub-) structure >- Display of the structure, at least in 2D (not just a name) >- Download/save a structure in a computer-readable format (SD, PDB...) >- Retrieve/dump large parts of the database (or even the entire DB) in > bulk form, again in a computer-readable format >- Perform some kind of calculation on the structure (e.g. physicochemical > properties etc.) >- At least 100 molecules available >- Accessible with just a Web browser, possibly with some easily obtainable > plugin (this excludes services that require a special application, such > as SciFinder) > >These sites may be academic, commercial, government, non-profit. Required >fees or subscription is not a disqualifier, but should be noted. > >I already have a certain number of such URLs; but I want to make sure >that I don't overlook anything. I'll post a summary of course. > >========================== ANSWERS ============================ >I got a few replies. Thanks to all who responded. >S Bear pointed out his own list, which proved to >be very useful for the compilation of our table. The three lists of links >I found most useful in this context are: >http://geocities.com/soaringbear/biomed/chem.html >http://www.liv.ac.uk/Chemistry/Links/refdatabases.html >http://chemfinder.cambridgesoft.com/siteslist.asp > >After quite a bit of additional hunting of my own, and trying to compare >features to some extent, I've decided not to post an unwieldy table on the >list. Instead, I have put up this table on our server, under: > >http://cactus.nci.nih.gov/ncidb2/chem_www.html. > >A note aside: Be forewarned - while testing all these sites, I experienced >numerous plugin incompatibilities, web browser (if not OS) crashes, >plugins "grabbing" files types/associations from each other etc. Now, >with all the very latest plugin versions installed, things seem to be a >bit more stable -- but this was not a wholly satisfactory experience... > >Marc > >------------------------------------------------------------------------ > Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick > E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 > Phone: (301) 846-5903 376 Boyles Street > Fax: (301) 846-6033 FREDERICK, MD 21702 USA > Head, Computer-Aided Drug Design MiniCore Facility > Laboratory of Medicinal Chemistry, Center for Cancer Research, > National Cancer Institute at Frederick, National Institutes of Health > http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm >------------------------------------------------------------------------ > > > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net ---------------------------------------------------------------------------------------------------------- Sudhakar Pamidighantam, Ph. D. Ph:217-333-5831 Fax:217-244-2909 NCSA @ UIUC, 4147 Beckman Institute email: spamidig@ncsa.uiuc.edu 405 N Mathews Ave. Urbana, Illinois 61801 WWW: swarna.ncsa.uiuc.edu -----------------------------------------------------------------------------------------------------------